That part (the "instantaneous effects" is referring to something, therefor it cannot be directly referred to. Because it is referring to the sentence before it, anything that modifies it will also modify the sentence before it. The sentence about the CL checks, regardless of whether it modifies the previous sentence or the first sentence, will modify the first sentence. I'm no english major, so my terms are messed up, but hopefully you get my point. And if I were the one writing that spell, you can be certain I would change the wording to be less confusing. I'd probably have all three of those sentences run together, in fact, separated by commas, so that it's all one thought. I would absolutely have had the "instantaneous effects ) be in the same sentence as the target, that way, since new sentence=new thought, the CL check would modify the whole previous sentence.